Katoh, Standley 2013 (Molecular Biology and Evolution 30:772-780)
MAFFT multiple sequence alignment software version 7: improvements in performance and usability.
(outlines version 7)

Katoh, Frith 2012 (Bioinformatics 28:3144-3146)
Adding unaligned sequences into an existing alignment using MAFFT and LAST.
(describes the --add and --addfragments options)

Katoh, Toh 2010 (Bioinformatics 26:1899-1900)
Parallelization of the MAFFT multiple sequence alignment program.
(describes the multithread version)

Katoh, Asimenos, Toh 2009 (Methods in Molecular Biology 537:39-64)
Multiple Alignment of DNA Sequences with MAFFT. In Bioinformatics for DNA Sequence Analysis edited by D. Posada
(outlines DNA alignment methods and several tips including group-to-group alignment and rough clustering of a large number of sequences)

Katoh, Toh 2008 (BMC Bioinformatics 9:212)
Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework.
(describes RNA structural alignment methods)

Katoh, Toh 2008 (Briefings in Bioinformatics 9:286-298)
Recent developments in the MAFFT multiple sequence alignment program.
(outlines version 6; Fast Breaking Paper in Thomson Reuters' ScienceWatch)

Katoh, Toh 2007 (Bioinformatics 23:372-374)  Errata
PartTree: an algorithm to build an approximate tree from a large number of unaligned sequences.
(describes the PartTree algorithm)

Katoh, Kuma, Toh, Miyata 2005 (Nucleic Acids Res. 33:511-518)
MAFFT version 5: improvement in accuracy of multiple sequence alignment.
(describes [ancestral versions of] the G-INS-i, L-INS-i and E-INS-i strategies)

Katoh, Misawa, Kuma, Miyata 2002 (Nucleic Acids Res. 30:3059-3066)
MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform.
(describes the FFT-NS-1, FFT-NS-2 and FFT-NS-i strategies) 
